I must confess to watching Stonewall's recent self-destruction with an element of schadenfreude. On hearing the news that it stands accused of opposing same-sex marriage, I had to look out of the window certain that a squadron of pigs must be flying past in perfect formation. Recent similar developments have also had me scanning the skies for airborne livestock.

Stonewall is an organisation that does not allow trans people to join, despite the fact that a lot of them were central to the 1969 Stonewall riots, a milestone that was the catalyst for the gay liberation movement. Stonewall has the right of freedom of association, and clearly does not wish to associate with us. Despite running its "diversity champions" programme, we are clearly not the sort of diversity Stonewall wants.

As well as its bizarre row over same-sex marriage, Stonewall has been in discussions with the government about issues related to transgender people and marriage. Transsexuals currently have to end existing marriages, usually against their will, as a condition of identy change in the form of a Gender Recognition Certificate. One spoke heart-wrenchingly about this at the Lib Dem conference last month, and how she and her partner hardly left each other's sight during the intervening period between their divorce and obtaining a civil partnership. That an organisation which excludes trans people has taken it upon itself to discuss with the government an issue central to the lives of many trans people behind our backs is nothing less than astonishing. But it doesn't stop there.

Fit, Stonewall's anti-homophobia film soon to be sent to all secondary schools, contains a short section about trans children. It does not actually include any trans children or young people, preferring instead to talk about trans people indirectly. In the film the term "tranny" is said to be "short for transgender". If Stonewall had consulted a couple of trans people they would have been left in no doubt that "tranny" is not short for transgender. It is the insult menacingly hurled at us in the street, along with thinly veiled threats. This rather wooden, one-dimensional portrayal of transgender people contrasts with the film's rich, deep and varied portrayal of LGB children. Once shown, this film will mean schools can consider themselves to have "done" LGBT equality. Yet a recent survey in America by the National Gay and Lesbian Task Force found that 41% of young trans people had attempted suicide, rising to 59% if their teacher was the perpetrator of abuse.

Stonewall Scotland, a separate organisation from Stonewall England, cited in a report published in 2007, a piece by Bill Leckie in the Scottish Sun as evidence of transphobia in the media. Now guess who, until yesterday, was nominated for the award of "journalist of the year" this year in their annual awards ceremony? Fortunately though, Stonewall saw sense over this one, and thanks to pressure by trans people, removed his name from the list of nominees yesterday.

Trans people still feel that Stonewall has crossed the line between excluding us and active denigration and promotion of transphobia. Stonewall has made the mistake of assuming that transgender don't matter. Trans people dream of achieving the level of social acceptance gay men and lesbians have today, yet Stonewall, in an act akin to pulling up the drawbridge behind them, is now actively undermining our efforts to achieve this. But transgender people are people. We can speak for ourselves, and hate crime against trans people is no different, in its effects, from any other form of hate crime. Including homophobia.

• This article was amended on 29 October 2010. The original said that transsexuals currently have to end existing marriages as a condition of surgery, usually against their will. This has been corrected.